The emulsion-solvent evaporation method has been widely employed as a route to achieve three-dimensional confined assembly for preparing block copolymer (BCP) microparticles. The interfacial property of emulsion droplets plays an important role in controlling the shapes and internal structures of the microparticles. In this report, we employed iron oxide nanoparticles (NPs) covered by pH-responsive poly(acrylic acid)-b-polystyrene (Fe3O4@PAA-b-PS) to control the oil/water interfacial interaction and the morphology of the resulting polystyrene-b-poly(dimethylsiloxane) (PS-b-PDMS) microparticles. A dramatic deformation of BCP microparticles from ellipsoidal Janus pupa-like particles to spherical onion-like particles was achieved by varying the location of Fe3O4@PAA-b-PS NPs through adjusting the pH value of the aqueous phase. The mechanism for the deformation was systemically investigated by varying the pH value of the aqueous phase, the weight fraction of Fe3O4@PAA-b-PS NPs in the oil phase, and the property of aqueous surfactants. Moreover, these Fe3O4-loaded hybrid BCP microparticles showed morphology-dependent T-2-weighted magnetic resonance imaging (MRI) performance, which may provide an alternative route to optimize the efficiency of MRI contrast agents.